Welcome to the PDBbind-CN Database!

Introduction. The aim of the PDBbind database is to provide a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank (PDB). It provides an essential linkage between the energetic and structural information of those complexes, which is helpful for various computational and statistical studies on molecular recognition, drug discovery, and many more (see the list of published applications of PDBbind).

The PDBbind database was originally developed by Prof. Shaomeng Wang's group at the University of Michigan in USA, which was first released to the public in May, 2004. This database is now maintained and further developed by Prof. Renxiao Wang's group at College of Pharmacy, Fudan University in China. The PDBbind database is updated on an annual base to keep up with the growth of the Protein Data Bank.


Invitation to the new PDBbind+ web site 02/03/2024

Current release. The current release, i.e. version 2020, is based on the contents of PDB officially released at the first week in 2020. This release provides binding affinity data for a total of 23,496 biomolecular complexes in PDB, including protein-ligand (19,443), protein-protein (2,852), protein-nucleic acid (1,052), and nucleic acid-ligand complexes (149). Compared to the last release (v.2019), binding data included in this release have increased by ~10%. All binding data are curated by ourselves from ~40,500 original references. Click here for a brief introduction to the PDBbind database (PDF).


A special remark on the PDBbind core set. Compilation of the PDBbind core set aims at providing a relatively small set of high-quality protein-ligand complexes for validating docking/scoring methods. The data set is selected based on the contents of PDBbind. In particular, this data set has served as the primary test set in the popular Comparative Assessment of Scoring Functions (CASF) benchmark developed by our group. The PDBbind core set is not included in the PDBbind data package because it is not updated annually as PDBbind itself. Users can obtain the PDBbind core set by downloading the CASF data package at http://www.pdbbind.org.cn/casf.php. The latest available version of the PDBbind core set is included in CASF-2016, which consists of 285 protein-ligand complexes.


Accessibility. The basic information of each complex in PDBbind is completely open for access (see the [BROWSE] page). Users are required to register under a license agreement in order to utilize the searching functions provided on this web site or to download PDBbind data sets in bulk. Registration is currently free of charge to all academic and industrial users. Please go to the [REGISTER] page and follow the instructions to complete registration.


Acknowledgments. This project is financially supported by the Ministry of Science and Technology of China (National Key Research Program, Grant No. 2016YFA0502302) and the National Natural Science Foundation of China (Grant No. 81725022, 81430083, 21661162003, 21673276, 21472227, 21472226). We are very grateful to Prof. Zenghui (John) Zhang's group at the East China Normal University for their aid to version 2015, 2016, and 2017.

News & Notice



PDBbind v2011 is released now (09/22/2011)

Dear researchers, We announce another release of the PDBbind database, i.e. version 2011. The PDBbind database aims at providing a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank. The PDBbind database was first released to the public in 2004 by Prof. Shaomeng Wang's group at the University of Michigan. It is now maintained and further developed by Prof. Renxiao Wang's group at the Shanghai Institute of Organic Chemistry. The PDBbind database is updated annually to keep up with the growth of the Protein Data Bank. This release, i.e. version 2011, provides binding affinity data for a total of 7,986 biomolecular complexes in PDB, including protein- ligand (6,051), nucleic acid-ligand (66), protein-nucleic acid (428), and protein-protein complexes (1,441), which is the largest collection of this kind so far. All binding data were carefully curated from original references rather than assembled from other data resources. Binding affinity data included in this release have increased by ~20% as compared to the last release (version 2010). Besides binding affinity data, ""clean"" processed structural files of the protein-ligand complexes in PDBbind are also provided for download. The PDBbind version 2011 is available on the PDBbind-CN web server at http://www.pdbbind-cn.org/. The basic information of each complex in PDBbind is accessible without the need of registration. Registration is required only if the users want to use the displaying and searching services provided on this web site or to download the data in PDBbind. Registration is free of charge for all academic and commercial/industrial users. More than 1,600 users from over 40 countries have already registered to use this database, and this number is still growing. We love to receive your comments on the PDBbind database so that we can improve it further. Best regards, Prof. Renxiao Wang & the whole PDBbind team Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai, P. R. China

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1. FAQs of the PDBbind-CN database
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4. Deposit binding affinity data into PDBbind-CN

Team Leader: Prof. Renxiao Wang
Email: wangrx@fudan.edu.cn
Tel: +86-21-54925128
Support: yingsaisi@foxmail.com

The PDBbind-CN Team Members

[1] Minyi Su, Qifan Yang, Yu Du, Guoqin Feng, Zhihai Liu, Yan Li,* Renxiao Wang,*, "Comparative Assessment of Scoring Functions: The CASF-2016 Update", J. Chem. Inf. Model, 2019, Vol. 59: pp 895-913.(CASF-2016)

[2] Yan Li, Minyi Su, Zhihai Liu, Jie Li, Jie Liu, Li Han, Renxiao Wang *, "Assessing Protein-Ligand Interaction Scoring Functions with the CASF-2013 Benchmark", Nature Protocols, 2018, Vol. 3(4): pp 666-680.(CASF-2013)

[3] Liu, Zhihai; Su, Minyi; Han, Li; Liu, Jie; Yang, Qifan; Li, Yan; Wang, Renxiao *, "Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions", Accounts of Chemical Research, 2017, 50 (2): pp. 302-309.(PDBbind version 2016)

[4] Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao, Wei Nie, Yuchen Liu and Renxiao Wang, "PDB-wide collection of binding data: current status of the PDBbind database", Bioinformatics, 2015, 31 (3): 405-412. (PDBbind version 2014)

[5] Li Y.; Liu Z.H.; Li J.; Han L.; Liu J.; Zhao Z.X.; Wang R.X. "Comparative Assessment of Scoring Functions on an Updated Benchmark: I. Compilation of the Test Set", J. Chem. Inf. Model., 2014, 54 (6), pp. 1700-1716. (PDBbind version 2013)

[6] Li, Y.; Han, L.; Liu, Z. H.; Wang, R. X.*. "Comparative Assessment of Scoring Functions on an Updated Benchmark: II. Evaluation Methods and General Results", J. Chem. Inf. Model., 2014, 54 (6), pp. 1717-1736. (CASF-2013)

[7] Cheng T.J.; Li X.; Li Y.; Liu Z.H.; Wang R.X. "Comparative assessment of scoring functions on a diverse test set", J. Chem. Inf. Model., 2009; 49(4); 1079-1093. (PDBbind version 2007)

[8] Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. "The PDBbind Database: Methodologies and updates", J. Med. Chem., 2005; 48(12); 4111-4119. (PDBbind prototype)

[9] Wang, R.; Fang, X.; Lu, Y.; Wang, S. "The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures", J. Med. Chem., 2004; 47(12); 2977-2980. (PDBbind prototype)

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